The crackdown followed a day of violence in which nine policemen and another 13 militants were killed in two separate attacks in the capital, Dushanbe, and in a nearby town.
"The militants were offered to surrender but they refused," an interior ministry spokesman told AFP.
"The operation of continues," he said of a joint police and army operation taking place on the ground and from the air.
Friday's attacks targeted a police post on the outskirts of Dushanbe, and a police station in Vahdat, which lies some 20 kilometres (13 miles) to the east.
The government claims the attacks were orchestrated by former deputy defence minister Abdulhalim Nazarzoda, who was dismissed from his position on Friday.
Those killed on Saturday died in a government attack on a remote mountain area some 50 kilometres northeast of the capital, officials said.
The security forces had also managed to recover more than 500 guns and ammunition, they added.
In a phone call with Tajik President Emomali Rakhmon, Russian President Vladimir Putin described Friday's attacks as "an attempt to destabilise" the country, a Kremlin spokesman said.
The Tajik government has said 51-year-old Nazarzoda -- who was dismissed "in connection with a crime" -- fought on the side of the United Tajik Opposition during the 1992-1997 civil war, which cost some 150,000 lives.
They did not give details on the alleged offence.
Officials have also said Nazarzoda belongs to the opposition Islamic Renaissance Party of Tajikistan (IRPT), which was effectively closed down by the government last week.
The IRPT has denied Nazarzoda is one of its members.
Nazarzoda, who took up the position of deputy defence minister in January, has worked at the ministry since 1999, when anti-government fighters were integrated into state institutions after the civil war.
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